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List Of Phylogenetic Tree Visualization Software
OneZoom This list of phylogenetic tree viewing software is a compilation of software tools and web portals used in visualizing phylogenetic trees. Online software Desktop software 1 "All" refers to Microsoft Windows, Apple OSX and Linux; L=Linux, M=Apple Mac, W=Microsoft Windows Libraries See also * List of phylogenetics software * Phylogenetics References {{reflist External links A 'comprehensive list' of Tree Editors Genetics databases phylog phylogenetics In biology, phylogenetics () is the study of the evolutionary history of life using observable characteristics of organisms (or genes), which is known as phylogenetic inference. It infers the relationship among organisms based on empirical dat ... Phylogenetics Visualization software Tree of life (biology) ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
OneZoom Hominidae
The OneZoom Tree of Life Explorer is a web application, web-based phylogenetic tree software. It aims to map the evolutionary connection of all known life. As of 2023 it includes over 2.2 million species. Organisation OneZoom was originally invented by James Rosindell and is a Charitable organization#United Kingdom, charity registered in London. It is sponsored by individuals such as Richard Dawkins. Tree of Life Explorer The design is based on the Pythagoras tree (fractal), pythagoras tree; beside a default spiral design there are other options, such as polytomy. Leaves and nodes provide links to other websites, such as Wikipedia, Encyclopedia of Life or the National Center for Biotechnology Information, NCBI taxonomy browser. The leaves representing single species are colour-coded according to their International Union for Conservation of Nature, IUCN extinction risk, with red indicating a threatened species, black representing a recently extinct species, and grey represen ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
NeighborNet
NeighborNet is an algorithm for constructing phylogenetic networks which is loosely based on the neighbor joining algorithm. Like neighbor joining, the method takes a distance matrix as input, and works by agglomerating clusters. However, the NeighborNet algorithm can lead to collections of clusters which overlap and do not form a hierarchy (mathematics), hierarchy, and are represented using a type of phylogenetic network called a Split graph, splits graph. If the distance matrix satisfies the Kalmanson combinatorial conditions then Neighbor-net will return the corresponding circular ordering. The method is implemented in the SplitsTree and R (programming language), R/Phangorn packages. Examples of the application of Neighbor-net can be found in virology, horticulture, dinosaur genetics, Quantitative comparative linguistics, comparative linguistics, and archaeology. References Computational phylogenetics Genetics software Molecular biology {{bioinformatics-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Lists Of Bioinformatics Software
A list is a set of discrete items of information collected and set forth in some format for utility, entertainment, or other purposes. A list may be memorialized in any number of ways, including existing only in the mind of the list-maker, but lists are frequently written down on paper, or maintained electronically. Lists are "most frequently a tool", and "one does not ''read'' but only ''uses'' a list: one looks up the relevant information in it, but usually does not need to deal with it as a whole".Lucie Doležalová,The Potential and Limitations of Studying Lists, in Lucie Doležalová, ed., ''The Charm of a List: From the Sumerians to Computerised Data Processing'' (2009). Purpose It has been observed that, with a few exceptions, "the scholarship on lists remains fragmented". David Wallechinsky, a co-author of ''The Book of Lists'', described the attraction of lists as being "because we live in an era of overstimulation, especially in terms of information, and lists help us ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Genetics Databases
Genetics is the study of genes, genetic variation, and heredity in organisms.Hartl D, Jones E (2005) It is an important branch in biology because heredity is vital to organisms' evolution. Gregor Mendel, a Moravian Augustinian friar working in the 19th century in Brno, was the first to study genetics scientifically. Mendel studied "trait inheritance", patterns in the way traits are handed down from parents to offspring over time. He observed that organisms (pea plants) inherit traits by way of discrete "units of inheritance". This term, still used today, is a somewhat ambiguous definition of what is referred to as a gene. Trait inheritance and molecular inheritance mechanisms of genes are still primary principles of genetics in the 21st century, but modern genetics has expanded to study the function and behavior of genes. Gene structure and function, variation, and distribution are studied within the context of the cell, the organism (e.g. dominance), and within the con ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Phylogenetics Software
This list of phylogenetics software is a compilation of computational phylogenetics software used to produce phylogenetic trees. Such tools are commonly used in comparative genomics, cladistics, and bioinformatics. Methods for estimating phylogenies include neighbor-joining, maximum parsimony (also simply referred to as parsimony), unweighted pair group method with arithmetic mean (UPGMA), Bayesian phylogenetic inference, maximum likelihood, and distance matrix methods. List See also * List of phylogenetic tree visualization software References External links *Complete list oInstitut Pasteurphylogeny webserversExPASyList of phylogenetics programs *A verof phylogenetic tools (reconstruction, visualization, ''etc.'') *Anothelist of evolutionary genetics software*A list ophylogenetic softwareprovided by the Zoological Research Museum A. Koenig *MicrobeTrace available at https://github.com/CDCgov/MicrobeTrace/wiki {{DEFAULTSORT:List Of Phylogenetics Software Geneti ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Phylogenetics
In biology, phylogenetics () is the study of the evolutionary history of life using observable characteristics of organisms (or genes), which is known as phylogenetic inference. It infers the relationship among organisms based on empirical data and observed heritable traits of DNA sequences, protein amino acid sequences, and morphology. The results are a phylogenetic tree—a diagram depicting the hypothetical relationships among the organisms, reflecting their inferred evolutionary history. The tips of a phylogenetic tree represent the observed entities, which can be living taxa or fossils. A phylogenetic diagram can be rooted or unrooted. A rooted tree diagram indicates the hypothetical common ancestor of the taxa represented on the tree. An unrooted tree diagram (a network) makes no assumption about directionality of character state transformation, and does not show the origin or "root" of the taxa in question. In addition to their use for inferring phylogenetic pa ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
List Of Phylogenetics Software
This list of phylogenetics software is a compilation of computational phylogenetics software used to produce phylogenetic trees. Such tools are commonly used in comparative genomics, cladistics, and bioinformatics. Methods for estimating phylogenies include neighbor-joining, maximum parsimony (also simply referred to as parsimony), unweighted pair group method with arithmetic mean ( UPGMA), Bayesian phylogenetic inference, maximum likelihood, and distance matrix methods. List See also * List of phylogenetic tree visualization software References External links *Complete list oInstitut Pasteurphylogeny webserversExPASyList of phylogenetics programs *A verof phylogenetic tools (reconstruction, visualization, ''etc.'') *Anothelist of evolutionary genetics software*A list ophylogenetic softwareprovided by the Zoological Research Museum A. Koenig *MicrobeTrace available at https://github.com/CDCgov/MicrobeTrace/wiki {{DEFAULTSORT:List Of Phylogenetics Software Gen ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cécile Ané
Cécile Ané is an evolutionary biologist, botanist, and statistical geneticist whose research involves the inference of evolutionary trees and the evolution of inherited traits, especially for plant species, as well as the mathematical statistics underlying these methods. Educated in France, she works in the United States as a professor at the University of Wisconsin–Madison, with joint appointments in the departments of botany and statistics. Education Ané is a graduate of the École normale supérieure de Lyon. She completed her Ph.D. in mathematics in 2000, at Toulouse III - Paul Sabatier University. Her dissertation, ''Grandes déviations et inégalités fonctionnelles pour des processus de Markov a temps continu sur un graphe'' 'Large deviations and functional inequalities for continuous-time Markov processes on a graph''concerned probability theory, and was directed by Michel Ledoux. Research After completing a doctorate in mathematics, Ané's research interests ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
BioPerl
BioPerl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It has played an integral role in the Human Genome Project. Background BioPerl is an active open source software project supported by the Open Bioinformatics Foundation. The first set of Perl codes of BioPerl was created by Tim Hubbard and Jong Bhak at MRC Centre Cambridge, where the first genome sequencing was carried out by Fred Sanger. MRC Centre was one of the hubs and birthplaces of modern bioinformatics as it had a large quantity of DNA sequences and 3D protein structures. Hubbard was using the th_lib.pl Perl library, which contained many useful Perl subroutines for bioinformatics. Bhak, Hubbard's first PhD student, created jong_lib.pl. Bhak merged the two Perl subroutine libraries into Bio.pl. The name BioPerl was coined jointly by Bhak and Steven Brenner at the Centre for Protein Engineering (CPE). In 1995, Brenner organized a BioPerl session at the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
UGENE
UGENE is computer software for bioinformatics. It helps biologists to analyze various biological genetics data, such as sequences, annotations, multiple alignments, phylogenetic trees, NGS assemblies, and others. UGENE integrates dozens of well-known biological tools, algorithms, and original tools in the context of genomics, evolutionary biology, virology, and other branches of life science. UGENE works on personal computer operating systems such as Windows, macOS, or Linux. It is released as free and open-source software, under a GNU General Public License (GPL) version 2. The data can be stored both locally and on shared/networked storage. The graphical user interface (GUI) provides access to pre-built tools so users with no computer programming experience can access those tools easily. UGENE also has a command-line interface to execute Workflows. Using UGENE Workflow Designer, it is possible to streamline a multi-step analysis. The workflow consists of blocks such as data r ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cladogram
A cladogram (from Greek language, Greek ''clados'' "branch" and ''gramma'' "character") is a diagram used in cladistics to show relations among organisms. A cladogram is not, however, an Phylogenetic tree, evolutionary tree because it does not show how ancestors are related to descendants, nor does it show how much they have changed, so many differing evolutionary trees can be consistent with the same cladogram. A cladogram uses lines that branch off in different directions ending at a clade, a group of organisms with a last common ancestor. There are many shapes of cladograms but they all have lines that branch off from other lines. The lines can be traced back to where they branch off. These branching off points represent a hypothetical ancestor (not an actual entity) which can be inferred to exhibit the traits shared among the terminal taxa above it. This hypothetical ancestor might then provide clues about the order of evolution of various features, adaptation, and other e ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
